dual-crispr-process-nf/nextflow.config at master · ZuberLab/dual-crispr-process-nf · GitHub

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nextflow.enable.dsl = 2

params {
    inputDir = 'raw'
    outputDir = 'results'
    library = 'library.txt'
	barcodes = 'barcodes.txt'
	barcode_demux_mismatches = 0
    barcode_demux_location =    'both'
	barcode_length = 4
    demux_unknown = false
	spacer_seq_R1 = 'ATATCCCTTGGAGAAAAGCCTTGTTT'
	spacer_seq_R2 = 'CTTGCTATGCACTCTTGTGCTTAGCTCTGAAAC'
    spacer_error_rate = 0.3
	guide_length = 21
	padding_bases_first_guide = 'GTT'
	padding_bases_matching_guide = 'ACC'
    random_barcode_length = 4
}

profiles {

    standard {
        includeConfig 'conf/resources.config'
    }

    apptainer {
        includeConfig 'conf/resources.config'
        includeConfig 'conf/apptainer.config'
    }

    cbe {
        includeConfig 'conf/resources.config'
        includeConfig 'conf/apptainer.config'
        includeConfig 'conf/cbe.config'
    }

    test {
        includeConfig 'conf/resources_test_mode.config'
        includeConfig 'conf/apptainer.config'
    }
}